3FV3 | pdb_00003fv3

Secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EAG	PDB ENTRY 1EAG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	five-fold molar inhibitor excess, Cpr=8mg/ml; drops: 0.002ml protein + 0.001ml reservoir + 0.0002ml 10mM ZnAc; reservoir: 0.1M Tris pH 7.0, 2.0M Ammonium Sulfate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.488	α = 90
b = 194.247	β = 91.52
c = 97.147	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	SBC-3		2008-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	50	99.3	0.045	27.2	3.8	274936	273011

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	98.5		0.49	2.4	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EAG	1.85	46.03	252690	269660	1368	99.99	0.16646	0.16634	0.17	0.19014	0.19	RANDOM	15.135

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.83		0.37	0.57		2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.701
r_dihedral_angle_4_deg	16.49
r_dihedral_angle_3_deg	12.185
r_dihedral_angle_1_deg	6.015
r_scangle_it	2.544
r_scbond_it	1.635
r_angle_refined_deg	1.256
r_mcangle_it	1.023
r_mcbond_it	0.61
r_nbtor_refined	0.302
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20582
Nucleic Acid Atoms
Solvent Atoms	2159
Heterogen Atoms	225

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling